Application Note: Amplicon Sequencing
NextSeq® 500 System Amplicon Sequencing Solution
A fast, easy, and accurate way to detect variants in a gene of interest across various sample types and species.
Highlights
• Fastest Sample-to-Data Amplicon Solution
Simple workflow with the lowest hands-on time
• Accurate Variant Detection
NextSeq System and TruSeq® Custom Amplicon assay deliver
high levels of multiplexing, excellent specificity and uniformity,
and high-quality data even through homopolymer regions
• Simple Assay Customization
DesignStudio™ enables selection of fixed or custom panels of
up to 1,536 amplicons in a single reaction, across a range of
amplicon sizes and reference genomes
• Easy, Flexible Data Analysis
Analysis performed in BaseSpace®, with VariantStudio offering a
robust method to enrich variant information with biological context
• End-to-End Illumina Support
Illumina scientists are there every step of the way, providing
installation, training, and applications support
Introduction
The NextSeq 500 System Amplicon Sequencing Solution enables
researchers to investigate targeted gene regions, identifying variants
rapidly and efficiently. It leverages industry-leading Illumina nextgeneration sequencing (NGS) technology, delivering the best data
quality and highest accuracy for detecting variants in genes of interest.
The NextSeq 500 System Amplicon Sequencing Solution includes
a web-based sequencing assay design tool for easy target region
selection and optimization, fully customizable library preparation assays
for targeted resequencing, and user-friendly data analysis software to
identify and classify disease-relevant variants quickly. With a seamless
sample-to-answer workflow, the NextSeq 500 System Amplicon
Sequencing Solution offers the flexibility to target expert-defined or
custom content for cancer, genetic disease, and population genetics
studies, and supports the discovery of somatic and germ line variants.
Figure1: NextSeq 500 System Sample-to-Answer
Amplicon Sequencing Workflow
Prep
Sequence
3 hours hands-on
10 minutes hands-on
8
15
HOURS
HOURS
Analyze
Share
5 minutes hands-on,
on-site or in cloud
Secure,
unlimited storage
0.5
HOURS PER SAMPLE
INSTANTLY
The simple NextSeq 500 workflow delivers highly accurate sequencing
data. Data analysis includes alignment and variant calling.
Base calls are generated on the NextSeq 500 System and data
analysis (including alignment and variant calling) can be performed with
the TruSeq Amplicon Core App in BaseSpace, the Illumina genomics
computing environment (Figure 2). With its intuitive interface accessed
through a common web browser, BaseSpace provides researchers
with access to a rich ecosystem of commercial and open-source DNA
data analysis software tools designed primarily to analyze Illumina
data. For example, variants can be further explored, interpreted, and
reported using VariantStudio, enabling researchers to identify variants
associated with a given phenotype.
The NextSeq 500 System also offers cross-application flexibility,
enabling researchers to transition easily from one sequencing project
to another (Figure 3). The system is fully compatible with the industry’s
widest range of library preparation kits from Illumina and third-parties,
enabling an easy transition between Illumina amplicon or larger
resequencing studies using TruSight® fixed panels*, transcriptome
(RNA-Seq), and whole-genome sequencing (WGS). For example,
researchers can pair amplicon sequencing with RNA-Seq to assess
whether identified variants alter transcript expression or expand their
studies with larger enrichment panels to explore areas beyond genes
of interest.
Figure 2: NextSeq 500 Sequencing System
A Simple, Customizable Amplicon
Sequencing Workflow
The NextSeq 500 amplicon sequencing workflow simplifies amplicon
sequencing, enabling researchers to maximize their productivity
(Figure 1). Researchers can create a custom amplicon panel using
DesignStudio and generate libraries with TruSeq Custom Amplicon
(TSCA) in one day. The dual sequencing output modes of the
NextSeq 500 Sequencing System and accompanying reagents deliver
20–120 Gb, enabling researchers to scale their amplicon panels and
study sizes accordingly.
The NextSeq 500 System leverages the latest advances in sequencing
by synthesis (SBS) chemistry and the industry’s simplest workflow.
*TruSight panels comprise oligo probes targeting genes and regions thought to
be relevant for particular diseases or conditions.
Application Note: Amplicon Sequencing
Figure 3: NextSeq 500 System
Sequencing Applications
Figure 4: DesignStudio Enables Easy Creation of
Custom Amplicon Sequencing Panels
Whole-Genome Sequencing
Amplicon Sequencing
RNA Sequencing
Exome Sequencing
The flexible NextSeq 500 System enables researchers to seamlessly
transition from one sequencing application to another to advance
their research.
Easy Amplicon Panel Customization
with DesignStudio
The NextSeq 500 System Amplicon Sequencing Solution supports
targeted resequencing of single exons, and fixed or custom panels.
TruSight fixed panels expedite research and conserve limited budgets
by assessing multiple genes simultaneously at approximately the same
cost as a single gene assay. For example, hematological cancers can
be studied using TruSight Myeloid, a fixed panel that employs TSCA
assay chemistry and consists of 54 genes mutated frequently in
myeloid malignancies.
Researchers can also use DesignStudio to create customized panels
with optimized content for their studies (Figure 4). This personalized,
easy-to-use, web-based assay design tool provides dynamic feedback
to enhance target region coverage, reducing the time required to
design custom projects. By building a custom panel, users can
focus their sequencing coverage on regions of interest and gain
more confidence in detection of germ line and somatic variants.
Using DesignStudio, researchers can create panels with a range of
amplicon sizes optimized for different sample types (e.g. formalin-fixed,
paraffin-embedded) and reference genomes (e.g. human, mouse, rat,
and bovine).
Integrated Library Preparation
TSCA is used to prepare custom amplicon panels for sequencing.
Following panel creation using DesignStudio, oligonucleotide probes
are synthesized at Illumina and pooled into a Custom Amplicon Tube.
The TSCA assay kit generates up to 1,536 amplicons per reaction,
Building custom amplicon panels in DesignStudio enables researchers to
sequence regions of interest to detect germ line and somatic variants.
incorporating integrated indexes to support up to 96 samples per
run. It allows researchers to sequence hundreds of genomic regions
covering as little as 2 kB or up to 650 kB of cumulative sequence.
Fast, Accurate Variant Detection
Leveraging Illumina NGS technology, the NextSeq 500 System delivers
industry-leading sequencing accuracy of > 75% of sequenced bases
over Q30* at 2 × 150 bp. It can successfully sequence even the most
difficult regions (GC-rich, homopolymers), yielding a higher percentage
of true variants than other high-throughput desktop sequencers
(Figure 5). Its low false positive and false negative rates drastically
reduce the time and cost of downstream validation. By offering the
highest data quality, the NextSeq 500 System is the best sequencing
system for capturing the full value of amplicon sequencing.
The easy workflow of the NextSeq 500 System simplifies amplicon
sequencing. It takes less than 20 minutes to load and initiate the
system. Sequencing of up to 96 samples is completed in as little as
26 hours. The flexible, scalable NextSeq 500 System with its dual
sequencing output modes (Mid and High) and ability to handle a
range of sample sizes enables researchers to tune and optimize their
amplicon studies easily (Table 1).
Based on industry-leading Illumina sequencing by synthesis chemistry,
the NextSeq 500 System enables researchers to compare and
integrate the data it generates with data from studies performed on
other Illumina systems. For example, NextSeq 500 System amplicon
sequencing data can be integrated with data generated on the Illumina
MiSeq® or HiSeq® Systems (Table 2).
Selecting Sequencing Depth for Amplicon Sequencing
Sequencing coverage (sensitivity) describes the average number of reads that align to, or “cover,” known reference bases. Coverage level
often determines whether variant discovery can be made with a certain degree of confidence at particular base positions. At higher levels
of coverage, each base is covered by a greater number of aligned sequence reads, so base calls can be made with a higher degree of
confidence. For example, higher coverage could enable detection of somatic variants that may be present at very low levels.
The following are coverage guidelines to achieve appropriate detection levels for certain studies:
• Heterozygote detection—40× coverage
• 5% variation of single-base changes and multi-base deletions—1000× coverage
• 1% variation of single-base changes and multi-base deletions— ≤ 5000× coverage
• Single-base indels may require additional depth
* Q30 = 1 error in 1,000 base calls or an accuracy of 99.9%
Application Note: Amplicon Sequencing
Figure 5: NextSeq 500 System Delivers High-Quality
Sequencing through Homopolymer Regions
The NextSeq 500 System can sequence successfully through GC-rich and
homopolymer regions to capture the full value of amplicon sequencing.
Table 1: NextSeq 500 System System Sequencing
Supports a Variety of Study Sizes
Panel Size
Average
Coverage
Depth
270 amplicons
Sequencing
Output
Samples
/ Run
≥ 5000×
2 × 150
(Mid Output)
96
1300 amplicons
≥ 1000×
2 × 150
(Mid Output)
96
1300 amplicons
≥ 5000×
2 × 150
(Mid Output)
24
1300 amplicons
≥ 5000×
2 × 150
(High Output)
72
Table 2: Illumina Amplicon Sequencing Solutions
Simplified Bioinformatics in BaseSpace
The Illumina BaseSpace environment removes much of the complexity
from the typical informatics workflow. Bases generated on the
NextSeq 500 System are instantly and securely transferred, analyzed,
and stored in BaseSpace (Cloud or Onsite), delivering annotated
variants in 30 minutes per sample. Researchers can choose to analyze
DNA data using the industry-standard BWA/GATK method or the
fast and accurate Illumina Isaac pipeline1. Analysis results, including
coverage statistics and annotated SNPs and indels are presented in
intuitive, easy-to-interpret reports.
Clinical researchers can use the VariantStudio application in
BaseSpace to identify and classify disease-relevant variants quickly.
Using a cascade of filtering options, researchers can rapidly isolate
the key variants that are consequential to the phenotype under study,
combining their expertise with provided annotations for rich variant
reports. Classified variants and associated information entered by the
user are saved to a local database so the information can be applied
easily to variants observed in other samples. VariantStudio offers
powerful report generation capabilities to communicate significant,
actionable findings concisely.
The BaseSpace environment also includes BaseSpace apps, a
growing community of software solutions for visualization, analysis,
and sharing. Because Illumina NGS technology is the most established
and broadly adopted sequencing solution, researchers can take
advantage of a large collection of commercial and open-source
sequencing analysis software designed primarily for processing
Illumina data. Through its intuitive user interface and this rich
ecosystem of third-party tools and apps, BaseSpace enables
researchers to identify known disease variants quickly.
Summary
The NextSeq 500 System Amplicon Sequencing Solution offers a fast
and easy sample-to-answer solution for identifying variants in gene
regions. Offering the flexibility of expert-defined fixed TruSight panels or
custom TruSeq panels created with DesignStudio, this unique solution
enables researchers to identify, evaluate, and classify gene variants
accurately. Rapid library preparation, industry-leading sequencing
accuracy, and simple data analysis enable researchers to identify
variants with clinical relevance and move their research forward faster.
Read Length
No. of
Samples
Average
Coverage
/ Sample
2 × 150 bp
16
1600×
NextSeq 500 System
Mid Output Flow Cell
2 × 150 bp
48
4300×
NextSeq 500 System
Mid Output Flow Cell
2 × 150 bp
96
2150×
NextSeq 500 System
High Output Flow Cell
2 × 150 bp
96
6500×
References
HiSeq 2500 System
Rapid Mode
2 × 150 bp
96
9700×
1. Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, et al.
(2013) Isaac: Ultra-fast whole genome secondary analysis on Illumina
sequencing platforms. Bioinformatics 29: 2041-2043.
Illumina Sequencing
System
MiSeq System
NextSeq 500 System Performance Parameters†
Flow Cell Configuration
Read Length (bp)
Output (Gb)
Run Time
Data Quality
High Output Flow Cell
2 × 150
100–120
29 hours
> 75% > Q30
Up to 400 M single reads
2 × 75
50–60
18 hours
> 80% > Q30
Up to 800 M paired-end reads
1 × 75
25–30
11 hours
> 80% > Q30
Mid Output Flow Cell
2 × 150
32.5–39
26 hours
> 75% > Q30
2 × 75
16.25–19.5
15 hours
> 80% > Q30
Up to 130 M single reads
Up to 260 M paired-end reads
Required Input
TruSeq Custom Amplicon Assay
≥ 50 ng High-Quality Genomic DNA
≥ 250 ng FFPE Genomic DNA
†
Total times include cluster generation, sequencing, and base calling on a NextSeq 500 System. Install specifications are based on Illumina PhiX control library at supported cluster
densities (between 129 and 165 K/mm² clusters passing filter). Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter. The percentage
of bases > Q30 is averaged over the entire run.
Application Note: Amplicon Sequencing
Ordering Information
Join the Illumina Community
With a NextSeq 500 system in their laboratory, researchers
join a worldwide community of over 60,000 scientists using
Illumina technology for their research studies. Illumina schedules
community events throughout the year, bringing researchers
together to share ideas. User group meetings, scientific
symposiums, and blog forums provide venues to discuss new
research methods and breakthrough studies.
An integral part of the Illumina community is our dedicated
service and support team, consisting of more than 300 people
worldwide, 75% of whom have advanced degrees. Illumina
technical support begins when the NextSeq 500 System is
delivered, with Illumina scientists and engineers assisting with
system installation and setup, and the training of laboratory
personnel. They are there 24/7 globally to answer questions
every step of the way, giving researchers the peace of mind to
focus on their next research study.
System Name
Catalog No.
NextSeq 500 Sequencing System
SY-415-1001
Output Kit Name
NextSeq 500 Mid Output Kit (150 cycles)
FC-404-1001
NextSeq 500 Mid Output Kit (300 cycles)
FC-404-1003
NextSeq 500 High Output Kit (75 cycles)
FC-404-1005
NextSeq 500 High Output Kit (150 cycles)
FC-404-1002
NextSeq 500 High Output Kit (300 cycles)
FC-404-1004
NextSeq 500 System Specifications
Instrument Configuration
RFID tracking for consumables
Instrument Control Computer (Internal)§
As researchers’ needs change, new systems are brought into
the laboratory, or new methods are undertaken, the Illumina
support and training teams are there to provide assistance. In
addition to on-site support, training courses (via webinar or at an
Illumina facility) are available to bring laboratory personnel quickly
up to speed.
Base Unit: Dual Intel Xeon ES-2448L 1.8 GHz CPU
Memory: 96 GB RAM
Hard Drive: 750 GB
Operating System: Windows 7 embedded standard
§
Computer specifications are subject to change.
Operating Environment
Temperature: 19°C to 25°C (22°C ± 3°C)
Humidity: Non-condensing 20%–80% relative humidity
Library Preparation Kits
Altitude: Less than 2,000 m (6,500 ft)
Air Quality: Pollution degree rating of II
Ventilation: Up to 2,048 BTU/hr @ 600 W
Kit
Catalog No.
TruSeq Custom Amplicon v1.5 Kit (96 samples)
FC-130-1001
Light Emitting Diode (LED)
TruSeq Custom Amplicon Index Kit
(96 indexes, 384 samples)
FC-130-1003
520 nm, 650 nm; Laser diode: 780 nm, Class IIIb
TruSeq Index Plate Fixture Kit
FC-130-1005
W×D×H: 58.5 cm × 53.4 cm × 63.5 cm (23.0 in × 21.0 in × 25 in)
TruSeq Index Plate Fixture and Collar Kit (2 each)
FC-130-1007
For Indoor Use Only
Dimensions
Weight: 83 kg (183 lbs)
Crated Weight: 151.5 kg (334 lbs)
Power Requirements
100–120 VAC 15 A
220–240 VAC 10 A
Radio Frequency Identifier (RFID)
Frequency: 13.56 MHz
Power: Supply current 120 mA, RF output power 200 mW
Product Safety and Compliance
NRTL certified IEC 61010-1
CE marked
FCC/IC approved
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For Research Use Only -OR- For In Vitro Diagnostic Use. Not available in all countries or regions.
© 2014 Illumina, Inc. All rights reserved.
Illumina, BaseSpace, DesignStudio, NextSeq, TruSeq, TruSight, and the pumpkin orange color are trademarks of Illumina, Inc.
and/or its affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their
respective owners.
Pub. No. 770-2014-027 Current as of 20 October 2014